Nrf2_landscape
Authors: Megan Chang*, Carter J. Wilson*, Nadun Chanaka Karunatilleke, Mohamed Hesham Moselhy, Mikko Karttunen, Wing-Yiu Choy
* = equal contribution
Abstract: The Nrf2-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CBP, mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here we performed 48\,$\mu$s of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments in order to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. The two main findings are the following: We find Neh5 to be markedly more disordered than Neh4, which shows a propensity to form a 9-residue $\alpha$-helix in the middle of the domain. Thus, pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4 which has no glutamic acid. The CHARMM36m force field agrees most closely with the CD results.